GraphScope Flex: LEGO-like Graph Computing Stack

Graph computing has become increasingly crucial in processing large-scale graph data, with numerous systems developed for this purpose. Two years ago, we introduced GraphScope as a system addressing a wide array of graph computing needs, including graph traversal, analytics, and learning in one system. Since its inception, GraphScope has achieved significant technological advancements and gained widespread adoption across various industries. However, one key lesson from this journey has been understanding the limitations of a "one-size-fits-all" approach, especially when dealing with the diversity of programming interfaces, applications, and data storage formats in graph computing. In response to these challenges, we present GraphScope Flex, the next iteration of GraphScope. GraphScope Flex is designed to be both resource-efficient and cost-effective, while also providing flexibility and user-friendliness through its LEGO-like modularity. This paper explores the architectural innovations and fundamental design principles of GraphScope Flex, all of which are direct outcomes of the lessons learned during our ongoing development process. We validate the adaptability and efficiency of GraphScope Flex with extensive evaluations on synthetic and real-world datasets. The results show that GraphScope Flex achieves 2.4X throughput and up to 55.7X speedup over other systems on the LDBC Social Network and Graphalytics benchmarks, respectively. Furthermore, GraphScope Flex accomplishes up to a 2,400X performance gain in real-world applications, demonstrating its proficiency across a wide range of graph computing scenarios with increased effectiveness

H(2) enhances arabidopsis salt tolerance by manipulating ZAT10/12-mediated antioxidant defence and controlling sodium exclusion.

BACKGROUND: The metabolism of hydrogen gas (H(2)) in bacteria and algae has been extensively studied for the interesting of developing H(2)-based fuel. Recently, H(2) is recognized as a therapeutic antioxidant and activates several signalling pathways in clinical trials. However, underlying physiological roles and mechanisms of H(2) in plants as well as its signalling cascade remain unknown. METHODOLOGY/PRINCIPAL FINDINGS: In this report, histochemical, molecular, immunological and genetic approaches were applied to characterize the participation of H(2) in enhancing Arabidopsis salt tolerance. An increase of endogenous H(2) release was observed 6 hr after exposure to 150 mM NaCl. Arabidopsis pretreated with 50% H(2)-saturated liquid medium, mimicking the induction of endogenous H(2) release when subsequently exposed to NaCl, effectively decreased salinity-induced growth inhibition. Further results showed that H(2) pretreatment modulated genes/proteins of zinc-finger transcription factor ZAT10/12 and related antioxidant defence enzymes, thus significantly counteracting the NaCl-induced reactive oxygen species (ROS) overproduction and lipid peroxidation. Additionally, H(2) pretreatment maintained ion homeostasis by regulating the antiporters and H(+) pump responsible for Na(+) exclusion (in particular) and compartmentation. Genetic evidence suggested that SOS1 and cAPX1 might be the target genes of H(2) signalling. CONCLUSIONS: Overall, our findings indicate that H(2) acts as a novel and cytoprotective regulator in coupling ZAT10/12-mediated antioxidant defence and maintenance of ion homeostasis in the improvement of Arabidopsis salt tolerance

Rapid regulation of the plasma membrane H+-ATPase activity is essential to salinity tolerance in two halophyte species, Atriplex lentiformis and Chenopodium quinoa

Background and Aims The activity of H+-ATPase is essential for energizing the plasma membrane. It provides the driving force for potassium retention and uptake through voltage-gated channels and for Na+ exclusion via Na+/H+ exchangers. Both of these traits are central to plant salinity tolerance; however, whether the increased activity of H+-ATPase is a constitutive trait in halophyte species and whether this activity is upregulated at either the transcriptional or post-translation level remain disputed. Methods The kinetics of salt-induced net H+, Na+ and K+ fluxes, membrane potential and AHA1/2/3 expression changes in the roots of two halophyte species, Atriplex lentiformis (saltbush) and Chenopodium quinoa (quinoa), were compared with data obtained from Arabidopsis thaliana roots. Key Results Intrinsic (steady-state) membrane potential values were more negative in A. lentiformis and C. quinoa compared with arabidopsis (−144 ± 3·3, −138 ± 5·4 and −128 ± 3·3 mV, respectively). Treatment with 100 mM NaCl depolarized the root plasma membrane, an effect that was much stronger in arabidopsis. The extent of plasma membrane depolarization positively correlated with NaCl-induced stimulation of vanadate-sensitive H+ efflux, Na+ efflux and K+ retention in roots (quinoa > saltbush > arabidopsis). NaCl-induced stimulation of H+ efflux was most pronounced in the root elongation zone. In contrast, H+-ATPase AHA transcript levels were much higher in arabidopsis compared with quinoa plants, and 100 mM NaCl treatment led to a further 3-fold increase in AHA1 and AHA2 transcripts in arabidopsis but not in quinoa. Conclusions Enhanced salinity tolerance in the halophyte species studied here is not related to the constitutively higher AHA transcript levels in the root epidermis, but to the plant’s ability to rapidly upregulate plasma membrane H+-ATPase upon salinity treatment. This is necessary for assisting plants to maintain highly negative membrane potential values and to exclude Na+, or enable better K+ retention in the cytosol under saline conditions

H₂ protects Arabidopsis seedlings against salt stress-induced lipid peroxidation and ROS homeostasis.

<p>Seedlings were pre-incubated in 50% H₂-saturated MS liquid medium for 24 hr, and then exposed to the MS liquid medium in the presence or absence of 150 mM NaCl. Sample without chemicals was the control (Con). Levels of lipid peroxidation (thiobarbituric acid reactive substance, TBARS) were measured at the indicated times (A). To detect O₂⁻ and H₂O₂, seedlings were stained with NBT (B) and DAB (C) 120 hr after various treatments, respectively. Bar  = 2 mm. (D) Transcript levels of <i>zinc finger protein10</i> (<i>ZAT10</i>; At1g27730), <i>zinc finger protein12</i> (<i>ZAT12</i>; At5g59820), <i>cytosolic ascorbate peroxidase1</i> (<i>cAPX1</i>, At1g07890) and <i>Fe superoxide dismutase1</i> (<i>FSD1</i>, Ag4g25100) after 120 hr of indicated treatments were analyzed by real-time RT-PCR. Expression levels were presented as values relative to corresponding untreated control samples (Con), after normalization to <i>actin2/7</i> (At3g18780) levels. Statistical analysis was performed using SPSS 16.0 software. Data are means ± SE from three independent experiments. Bars with different letters are significantly different at <i>P</i><0.05 according to Duncan’s multiple range test.</p

Regulation of transcripts responsible for Na compartmentation by H₂.

<p>(A, B) Relative gene expression of <i>Arabidopsis V-type proton ATPase proteolipid subunit c4</i> (<i>AVAP4</i>; At1g75630), <i>sodium hydrogen exchanger2</i> (<i>NHX2</i>; At3g05030), <i>sodium hydrogen exchanger5</i> (<i>NHX5</i>; At1g54370), <i>Arabidopsis vacuolar membrane proton pump1</i> (<i>AVP1</i>; At1g15690), <i>sodium hydrogen exchanger1</i> (<i>NHX1</i>; At5g27150), and <i>sodium hydrogen exchanger3</i> (<i>NHX3</i>; At5g55470) in Arabidopsis seedling roots or leaves, respectively. Seedlings were pre-incubated in 50% H₂-saturated MS liquid medium for 24 hr, and then exposed to the MS liquid medium in the presence or absence of 150 mM NaCl for anther 120 hr. Sample without chemicals was the control (Con). Plot key illustrated each bar shown in A and B. Statistical analysis was performed using SPSS 16.0 software. Data are means ± SE from three independent experiments. Differences among treatments were analyzed by one-way ANOVA, taking <i>P</i><0.05 level as significant according to Duncan’s multiple range test.</p

Modulation of APX by H₂ and phenotypes of <i>cAPX1</i> knockout plants.

<p>(A) Changes of APX activity in Arabidopsis seedlings. (B) Up panel, stromal APX (sAPX) and cytoplasmic APX (cAPX) gene expression in Arabidopsis seedlings. Bottom panel, Coomassie Brilliant Blue-stained gels that showing equal amounts of proteins were loaded. The numbers above/below the band indicate the relative abundance of the corresponding sAPX/cAPX protein compared with that of the control sample. (C) Determination of total APX activity in 5-day-old wild-type and <i>capx1</i> mutant seedlings. (D–F) Changes of fresh weight, chlorophyll content, and primary root growth of <i>capx1</i> mutant seedlings. Corresponding samples without chemicals were regarded as a control (Con, 100%). 5-day-old wild-type and <i>capx1</i> mutant seedlings were pretreated with or without 50% H₂-saturated aqueous solution for 24 hr, followed by the exposure to the liquid MS medium in the presence or absence of 150 mM NaCl for another 120 hr, and then phenotypic indicators were determined, respectively. The dashed lines denoted the inhibition rate of wild-type grown under NaCl stress, taking corresponding wild-type samples without chemicals as a 100%. Statistical analysis was performed using SPSS 16.0 software. Data are means ± SE from three independent experiments. Bars denoted by the different letters were different significantly at <i>P</i><0.05 according to Duncan’s multiple range test (A, D-F). Additionally, the asterisk above the bar indicates significantly different in comparison with the wild-type at <i>P</i><0.05 according to <i>t</i> test (C).</p

H₂ regulates ion homeostasis and phenotypes of <i>sos1</i> knockout plants.

<p>(A) Changes of Na/K ratio in Arabidopsis seedlings. (B) Relative gene expression of <i>salt overly sensitive1</i> (<i>SOS1</i>; At2g01980), <i>Arabidopsis H⁺-ATPase3</i> (<i>AHA3</i>; At5g57350) in Arabidopsis seedling roots. (C) Up panel, plasma membrane (PM) H⁺-ATPase protein level in Arabidopsis seedling roots. Bottom panel, Coomassie Brilliant Blue-stained gels that showing equal amounts of proteins were loaded. The number above the band indicates the relative abundance of the corresponding H⁺-ATPase_protein compared with that of the control sample. (D-F) Changes of fresh weight, chlorophyll content, and primary root growth of <i>sos1</i> mutant seedlings. Corresponding samples without chemicals were regarded as a control (Con, 100%). 5-day-old wild-type and <i>sos1</i> mutant seedlings were pretreated with or without 50% H₂-saturated aqueous solution for 24 hr, followed by the exposure to the liquid MS medium in the presence or absence of 150 mM NaCl for another 120 hr, and then phenotypic indicators were determined, respectively. The dashed lines denoted the inhibition rate of wild-type grown under NaCl, taking corresponding wild-type samples without chemicals as a 100%. Statistical analysis was performed using SPSS 16.0 software. Data are means ± SE from three independent experiments. The asterisk above the bar indicates significantly different in comparison with NaCl-treated alone sample at <i>P</i><0.05 according to <i>t</i> test (A). Additionally, bars denoted by the different letters were different significantly at <i>P</i><0.05 according to Duncan’s multiple range test (B, D–F).</p

H₂ alleviates salt stress-induced Arabidopsis seedlings growth inhibition.

<p>Effects of H₂-saturated aqueous solution pretreatments with the indicated saturations for 24 hr on endogenous H₂ production (A), fresh weight and primary root growth (B) in 5-day-old seedlings grown in the liquid MS medium with or without NaCl treatment for the indicated times (A) or 120 hr (B). Effects of H₂ pretreatment on morphology (C), chlorophyll content and fresh weight (D) in Arabidopsis plants. 25-day-old seedlings were pretreated with or without 50% H₂-saturated aqueous solution for 24 hr and then exposed to the liquid MS medium in the presence or absence of 150 mM NaCl for another 8 days. Sample without chemicals was the control (Con). Bar  = 2 cm (C). Statistical analysis was performed using SPSS 16.0 software. Data are means ± SE from three independent experiments. Bars with different letters are significantly different at <i>P</i><0.05 according to Duncan’s multiple range test.</p